Locus 1742

Sequence ID dm3.chr2L
Location 13,465,375 – 13,465,487
Length 112
Max. P 0.749536
window2390 window2391

overview

Window 0

Location 13,465,375 – 13,465,483
Length 108
Sequences 7
Columns 111
Reading direction reverse
Mean pairwise identity 62.94
Shannon entropy 0.74223
G+C content 0.36137
Mean single sequence MFE -25.37
Consensus MFE -7.48
Energy contribution -9.03
Covariance contribution 1.55
Combinations/Pair 1.47
Mean z-score -1.66
Structure conservation index 0.29
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.58
SVM RNA-class probability 0.749536
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 13465375 108 - 23011544
CCUGGUCUACAGAUAUUGCAUUUGUUGCAAUGCAAAUGCAGCGAGGCUUUUAAGACCGAACUAUAAAUUGGAUUUCUUUUUACCGGAAGCGG---AAAUGUUUGUAGAAAU
.....((((((((((((((.(((((((((.......)))))))))))........((((........))))...........(((....)))---.))))))))))))... ( -30.60, z-score =  -2.79, R)
>droAna3.scaffold_12943 2169599 92 - 5039921
------------------CAGGCUUCA-GGAGCGAGAGCAAAUCGAGUGUGAGUGCGGCUGUAAAUUUUAUUUUUUUCUUUCCAAGAACUUGUUCAAGUCAUGGUAAGAUU
------------------(((((((((-.(..(((.......)))..).)))).))..)))...............((((.(((.((.(((....))))).))).)))).. ( -18.00, z-score =   0.76, R)
>droEre2.scaffold_4929 14657833 108 + 26641161
CCUGGUCUGCAGAUACUUUAUUUGUUGCAGUGCAAAUGCAGCGCGGCUUUUAAGACCUAACUAUAAAUUGGAUUUCUAUUUACCAAAAGCGG---AAAUCUUUGUAGAAAU
...((((((((((((...))))))).((.((((.......)))).)).....)))))...((((((...(((((((..(((.....)))..)---)))))))))))).... ( -27.90, z-score =  -2.00, R)
>droYak2.chr2L 9893555 108 - 22324452
CCUGGUCUACAGAUAUUGUGUUUGUUGCAAUGCAAAUGCAGCGAGGCUUUUAAGACCAAACUAUAAAUUGCAUUUCUAUUUACCAGAAGUGG---AAAUAUUUGUAGGAAU
..((((((((((...)))).(((((((((.......))))))))).......))))))..((((((((...((((((((((.....))))))---)))))))))))).... ( -29.00, z-score =  -2.45, R)
>droSec1.super_16 1611420 108 - 1878335
CCUGGUCUACAGAUAUUGCAUUUGUUGCAAUGCAAAUGCAGAGAGGCUUUUAAGACCGAACUAUAAAUUGGAUUUCUAUUUAGCAGAAGCGG---AAAUGUGUGUAGAAAU
.....((((((.(((((((((((((......))))))))................(((..((.(((((.((....)))))))..))...)))---.))))).))))))... ( -27.50, z-score =  -1.86, R)
>droSim1.chr2L 13247682 106 - 22036055
CCUGGUCUACAGAUAUUGCAUUUGUUGCAAUGCAAAUGCAGUGAGGCUUUUAAGACCGAACUAUAAAUUGGAUUUCUAUUC--CAGAAACGG---AAAUGUUUGUAGAAAU
.....((((((((((((((((((((......))))))))(((..((((....)).))..))).....(((((.......))--)))......---.))))))))))))... ( -31.20, z-score =  -3.67, R)
>droMoj3.scaffold_6500 3304042 91 + 32352404
------CAGCACUUUCAGCAGUUUUCACUUGGAAAUAACUUUAUGAGUUUGAAG--CUAGUUAAAUAAUUGAUUUCAUUUAACUAAUUUUGA---UGGCCUU---------
------..((((((..((..((((((....))))))..))....))))(..(((--.(((((((((.(......).))))))))).)))..)---..))...--------- ( -13.40, z-score =   0.41, R)
>consensus
CCUGGUCUACAGAUAUUGCAUUUGUUGCAAUGCAAAUGCAGCGAGGCUUUUAAGACCGAACUAUAAAUUGGAUUUCUAUUUACCAGAAGCGG___AAAUCUUUGUAGAAAU
...(((((..((...((((((((((......)))))))))).....))....)))))...................................................... ( -7.48 =  -9.03 +   1.55)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,465,379 – 13,465,487
Length 108
Sequences 7
Columns 111
Reading direction reverse
Mean pairwise identity 61.10
Shannon entropy 0.78813
G+C content 0.36930
Mean single sequence MFE -23.60
Consensus MFE -7.90
Energy contribution -9.51
Covariance contribution 1.62
Combinations/Pair 1.47
Mean z-score -1.04
Structure conservation index 0.33
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.09
SVM RNA-class probability 0.539458
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 13465379 108 - 23011544
CAGACCUGGUCUACAGAUAUUGCAUUUGUUGCAAUGCAAAUGCAGCGAGGCUUUUAAGACCGAACUAUAAAUUGGAUUUCUUUUUACCGGAAGCGGAAAUGUUUGUAG---
..........(((((((((((((.(((((((((.......)))))))))))........((((........))))...........(((....))).)))))))))))--- ( -27.80, z-score =  -1.76, R)
>droAna3.scaffold_12943 2169603 92 - 5039921
------------------CAGGCAGGCUUCA-GGAGCGAGAGCAAAUCGAGUGUGAGUGCGGCUGUAAAUUUUAUUUUUUUCUUUCCAAGAACUUGUUCAAGUCAUGGUAA
------------------..(((..((((((-.(..(((.......)))..).)))).)).))).....................(((.((.(((....))))).)))... ( -17.30, z-score =   1.38, R)
>droEre2.scaffold_4929 14657837 108 + 26641161
CAAACCUGGUCUGCAGAUACUUUAUUUGUUGCAGUGCAAAUGCAGCGCGGCUUUUAAGACCUAACUAUAAAUUGGAUUUCUAUUUACCAAAAGCGGAAAUCUUUGUAG---
.......((((((((((((...))))))).((.((((.......)))).)).....)))))...((((((...(((((((..(((.....)))..)))))))))))))--- ( -26.80, z-score =  -1.77, R)
>droYak2.chr2L 9893559 108 - 22324452
CAAGCCUGGUCUACAGAUAUUGUGUUUGUUGCAAUGCAAAUGCAGCGAGGCUUUUAAGACCAAACUAUAAAUUGCAUUUCUAUUUACCAGAAGUGGAAAUAUUUGUAG---
.((((((.((..........(((((((((......))))))))))).))))))...........((((((((...((((((((((.....))))))))))))))))))--- ( -28.10, z-score =  -2.02, R)
>droSec1.super_16 1611424 108 - 1878335
CAAACCUGGUCUACAGAUAUUGCAUUUGUUGCAAUGCAAAUGCAGAGAGGCUUUUAAGACCGAACUAUAAAUUGGAUUUCUAUUUAGCAGAAGCGGAAAUGUGUGUAG---
..........(((((.(((((((((((((......))))))))................(((..((.(((((.((....)))))))..))...))).))))).)))))--- ( -24.70, z-score =  -0.82, R)
>droSim1.chr2L 13247686 106 - 22036055
CAAACCUGGUCUACAGAUAUUGCAUUUGUUGCAAUGCAAAUGCAGUGAGGCUUUUAAGACCGAACUAUAAAUUGGAUUUCUAUUC--CAGAAACGGAAAUGUUUGUAG---
......((((((..((.((((((((((((......))))))))))))...))....))))))..(((((((((((....)))(((--(......))))..))))))))--- ( -28.60, z-score =  -2.79, R)
>droMoj3.scaffold_6500 3304046 91 + 32352404
------AAAACAGCACUUUCAGCAGUUUUCACUUGGAAAUAACUUUAUGAGUUUGAAG--CUAGUUAAAUAAUUGAUUUCAUUUAACUAAUUUUGAUGG------------
------........((((..((..((((((....))))))..))....))))(..(((--.(((((((((.(......).))))))))).)))..)...------------ ( -11.90, z-score =   0.52, R)
>consensus
CAAACCUGGUCUACAGAUAUUGCAUUUGUUGCAAUGCAAAUGCAGCGAGGCUUUUAAGACCGAACUAUAAAUUGGAUUUCUAUUUACCAGAAGCGGAAAUGUUUGUAG___
.......(((((..((...((((((((((......)))))))))).....))....))))).................................................. ( -7.90 =  -9.51 +   1.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:37:54 2011